3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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16 * PURPOSE. See the GNU General Public License for more details.
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23 <title>Colour Schemes</title>
24 <style type="text/css">
27 font-family: "Courier New", Courier, mono;
36 <strong>Colour schemes</strong>
38 <p>Jalview allows the user to set a colour scheme for the
39 whole alignment view or for each group defined on regions within it.</p>
40 <p>To change the colour for a view, simply select a new colour scheme from
41 the "Colour" menu.</p>
42 <p>To change the colour of a group, right click on any residue
43 within a group and use the popup menu to define the group colour.</p>
44 <p>At the top of the "Colour" menu you'll see a tick box
45 "Apply Colour to all groups". This is ticked by
46 default so that a chosen colour scheme will be applied to all
47 existing groups. If you wish to maintain the colour scheme for
48 defined groups, make sure you deselect this option before selecting
49 a new scheme in the Colour menu.</p>
51 The <strong>"Colour→<a
52 href="../colourSchemes/textcolour.html">Colour Text...</a>"
53 </strong> entry opens a dialog box to set a different text colour for light
54 and dark background, and the intensity threshold for transition
57 <p>The default colour schemes are summarised in the table below:
61 <strong>Protein Colour Schemes</strong>
94 <td height="24">Clustal</td>
95 <td bgcolor="#80a0f0"></td>
96 <td bgcolor="#f01505"></td>
97 <td bgcolor="#00ff00"></td>
98 <td bgcolor="#c048c0"></td>
99 <td bgcolor="#f08080"></td>
100 <td bgcolor="#00ff00"></td>
101 <td bgcolor="#c048c0"></td>
102 <td bgcolor="#f09048"></td>
103 <td bgcolor="#15a4a4"></td>
104 <td bgcolor="#80a0f0"></td>
105 <td bgcolor="#80a0f0"></td>
106 <td bgcolor="#f01505"></td>
107 <td bgcolor="#80a0f0"></td>
108 <td bgcolor="#80a0f0"></td>
109 <td bgcolor="#ffff00"></td>
110 <td bgcolor="#00ff00"></td>
111 <td bgcolor="#00ff00"></td>
112 <td bgcolor="#80a0f0"></td>
113 <td bgcolor="#15a4a4"></td>
114 <td bgcolor="#80a0f0"></td>
120 <td height="24">Zappo</td>
121 <td bgcolor="#ffafaf"></td>
122 <td bgcolor="#6464ff"></td>
123 <td bgcolor="#00ff00"></td>
124 <td bgcolor="#ff0000"></td>
125 <td bgcolor="#ffff00"></td>
126 <td bgcolor="#00ff00"></td>
127 <td bgcolor="#ff0000"></td>
128 <td bgcolor="#ff00ff"></td>
129 <td bgcolor="#6464ff"></td>
130 <td bgcolor="#ffafaf"></td>
131 <td bgcolor="#ffafaf"></td>
132 <td bgcolor="#6464ff"></td>
133 <td bgcolor="#ffafaf"></td>
134 <td bgcolor="#ffc800"></td>
135 <td bgcolor="#ff00ff"></td>
136 <td bgcolor="#00ff00"></td>
137 <td bgcolor="#00ff00"></td>
138 <td bgcolor="#ffc800"></td>
139 <td bgcolor="#ffc800"></td>
140 <td bgcolor="#ffafaf"></td>
147 <td bgcolor="#ccff00"></td>
148 <td bgcolor="#0000ff"></td>
149 <td bgcolor="#cc00ff"></td>
150 <td bgcolor="#ff0000"></td>
151 <td bgcolor="#ffff00"></td>
152 <td bgcolor="#ff00cc"></td>
153 <td bgcolor="#ff0066"></td>
154 <td bgcolor="#ff9900"></td>
155 <td bgcolor="#0066ff"></td>
156 <td bgcolor="#66ff00"></td>
157 <td bgcolor="#33ff00"></td>
158 <td bgcolor="#6600ff"></td>
159 <td bgcolor="#00ff00"></td>
160 <td bgcolor="#00ff66"></td>
161 <td bgcolor="#ffcc00"></td>
162 <td bgcolor="#ff3300"></td>
163 <td bgcolor="#ff6600"></td>
164 <td bgcolor="#00ccff"></td>
165 <td bgcolor="#00ffcc"></td>
166 <td bgcolor="#99ff00"></td>
172 <td>Hydrophobicity</td>
173 <td bgcolor="#ad0052"></td>
174 <td bgcolor="#0000ff"></td>
175 <td bgcolor="#0c00f3"></td>
176 <td bgcolor="#0c00f3"></td>
177 <td bgcolor="#c2003d"></td>
178 <td bgcolor="#0c00f3"></td>
179 <td bgcolor="#0c00f3"></td>
180 <td bgcolor="#6a0095"></td>
181 <td bgcolor="#1500ea"></td>
182 <td bgcolor="#ff0000"></td>
183 <td bgcolor="#ea0015"></td>
184 <td bgcolor="#0000ff"></td>
185 <td bgcolor="#b0004f"></td>
186 <td bgcolor="#cb0034"></td>
187 <td bgcolor="#4600b9"></td>
188 <td bgcolor="#5e00a1"></td>
189 <td bgcolor="#61009e"></td>
190 <td bgcolor="#5b00a4"></td>
191 <td bgcolor="#4f00b0"></td>
192 <td bgcolor="#f60009"></td>
193 <td bgcolor="#0c00f3"></td>
194 <td bgcolor="#680097"></td>
195 <td bgcolor="#0c00f3"></td>
198 <td>Helix Propensity</td>
199 <td bgcolor="#e718e7"></td>
200 <td bgcolor="#6f906f"></td>
201 <td bgcolor="#1be41b"></td>
202 <td bgcolor="#778877"></td>
203 <td bgcolor="#23dc23"></td>
204 <td bgcolor="#926d92"></td>
205 <td bgcolor="#ff00ff"></td>
206 <td bgcolor="#00ff00"></td>
207 <td bgcolor="#758a75"></td>
208 <td bgcolor="#8a758a"></td>
209 <td bgcolor="#ae51ae"></td>
210 <td bgcolor="#a05fa0"></td>
211 <td bgcolor="#ef10ef"></td>
212 <td bgcolor="#986798"></td>
213 <td bgcolor="#00ff00"></td>
214 <td bgcolor="#36c936"></td>
215 <td bgcolor="#47b847"></td>
216 <td bgcolor="#8a758a"></td>
217 <td bgcolor="#21de21"></td>
218 <td bgcolor="#857a85"></td>
219 <td bgcolor="#49b649"></td>
220 <td bgcolor="#758a75"></td>
221 <td bgcolor="#c936c9"></td>
224 <td nowrap>Strand Propensity</td>
225 <td bgcolor="#5858a7"></td>
226 <td bgcolor="#6b6b94"></td>
227 <td bgcolor="#64649b"></td>
228 <td bgcolor="#2121de"></td>
229 <td bgcolor="#9d9d62"></td>
230 <td bgcolor="#8c8c73"></td>
231 <td bgcolor="#0000ff"></td>
232 <td bgcolor="#4949b6"></td>
233 <td bgcolor="#60609f"></td>
234 <td bgcolor="#ecec13"></td>
235 <td bgcolor="#b2b24d"></td>
236 <td bgcolor="#4747b8"></td>
237 <td bgcolor="#82827d"></td>
238 <td bgcolor="#c2c23d"></td>
239 <td bgcolor="#2323dc"></td>
240 <td bgcolor="#4949b6"></td>
241 <td bgcolor="#9d9d62"></td>
242 <td bgcolor="#c0c03f"></td>
243 <td bgcolor="#d3d32c"></td>
244 <td bgcolor="#ffff00"></td>
245 <td bgcolor="#4343bc"></td>
246 <td bgcolor="#797986"></td>
247 <td bgcolor="#4747b8"></td>
250 <td>Turn Propensity</td>
251 <td bgcolor="#2cd3d3"></td>
252 <td bgcolor="#708f8f"></td>
253 <td bgcolor="#ff0000"></td>
254 <td bgcolor="#e81717"></td>
255 <td bgcolor="#a85757"></td>
256 <td bgcolor="#3fc0c0"></td>
257 <td bgcolor="#778888"></td>
258 <td bgcolor="#ff0000"></td>
259 <td bgcolor="#708f8f"></td>
260 <td bgcolor="#00ffff"></td>
261 <td bgcolor="#1ce3e3"></td>
262 <td bgcolor="#7e8181"></td>
263 <td bgcolor="#1ee1e1"></td>
264 <td bgcolor="#1ee1e1"></td>
265 <td bgcolor="#f60909"></td>
266 <td bgcolor="#e11e1e"></td>
267 <td bgcolor="#738c8c"></td>
268 <td bgcolor="#738c8c"></td>
269 <td bgcolor="#9d6262"></td>
270 <td bgcolor="#07f8f8"></td>
271 <td bgcolor="#f30c0c"></td>
272 <td bgcolor="#7c8383"></td>
273 <td bgcolor="#5ba4a4"></td>
276 <td>Buried Index</td>
277 <td bgcolor="#00a35c"></td>
278 <td bgcolor="#00fc03"></td>
279 <td bgcolor="#00eb14"></td>
280 <td bgcolor="#00eb14"></td>
281 <td bgcolor="#0000ff"></td>
282 <td bgcolor="#00f10e"></td>
283 <td bgcolor="#00f10e"></td>
284 <td bgcolor="#009d62"></td>
285 <td bgcolor="#00d52a"></td>
286 <td bgcolor="#0054ab"></td>
287 <td bgcolor="#007b84"></td>
288 <td bgcolor="#00ff00"></td>
289 <td bgcolor="#009768"></td>
290 <td bgcolor="#008778"></td>
291 <td bgcolor="#00e01f"></td>
292 <td bgcolor="#00d52a"></td>
293 <td bgcolor="#00db24"></td>
294 <td bgcolor="#00a857"></td>
295 <td bgcolor="#00e619"></td>
296 <td bgcolor="#005fa0"></td>
297 <td bgcolor="#00eb14"></td>
298 <td bgcolor="#00b649"></td>
299 <td bgcolor="#00f10e"></td>
307 <strong>Nucleotide Colour Schemes</strong>
330 <!--Unknown Purine-->
332 <!--Unknown Pyrimidine-->
336 <!--Weak nucleotide (A or T)-->
338 <!--Strong nucleotide (G or C)-->
340 <!--Amino (A or C)-->
344 <!--Not A (G or C or T)-->
346 <!--Not G (A or C or T)-->
348 <!--Not C (A or G or T)-->
350 <!--Not T (A or G or C-->
353 <td height="24">Nucleotide</td>
354 <td bgcolor="#64F73F"></td>
355 <td bgcolor="#FFB340"></td>
356 <td bgcolor="#EB413C"></td>
357 <td bgcolor="#3C88EE"></td>
358 <td bgcolor="#3C88EE"></td>
374 <td height="24">Purine/Pyrimidine</td>
375 <td bgcolor="#FF83FA"></td>
376 <td bgcolor="#40E0D0"></td>
377 <td bgcolor="#FF83FA"></td>
378 <td bgcolor="#40E0D0"></td>
379 <td bgcolor="#40E0D0"></td>
382 <td bgcolor="#FF83FA"></td>
383 <td bgcolor="#40E0D0"></td>
401 <p align="center"> </p>